The chain, known for its single-origin coffee and food made with local ingredients, was selected as the new operator after the museum put out a request last fall for someone new at the space, which overlooks the Unisphere.
The plan was to expand the food options at the museum and inside the park, and also eventually have outdoor seating.
Coffeed launched on Sunday at the premiere of the museum's new spring exhibit, which features the work of Italian Marinella Senatore.
Founder Frank "Turtle" Raffaele said the shop looks forward to bringing its food and drinks to a new audience at the museum, and plans to give a portion of the cafe's proceeds to the Flushing Meadows-Corona Park Alliance.
"To grow up in Queens and now be able to service and reflect the wonderful diversity of the borough is a true blessing for Coffeed," he said in a statement.